package ie.dcu.apps.ist.labelling;

import ie.dcu.apps.ist.AppWindow;

import java.io.BufferedReader;
import java.io.InputStreamReader;
import java.io.StringReader;
import java.net.HttpURLConnection;
import java.net.URL;
import java.net.URLEncoder;
import java.util.ArrayList;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

import javax.xml.bind.DatatypeConverter;

import javax.xml.parsers.*;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import org.xml.sax.InputSource;

import org.json.JSONArray;
import org.json.JSONObject;

public class Labels
{
	/**
	 * Function for getting the Labels through web service
	 * 
	 * @param
	 * The user entered text in the html element
	 * @return 
	 * ArrayList<String> containing each Label item
	 * 
	 */
	public ArrayList<OntologyTerm> getOntologyTerms(String content) {
        ArrayList<OntologyTerm> terms = new ArrayList<OntologyTerm>();
		// temporary variable for storing each list element in the loop
		try
	    {
			String encodedContent = URLEncoder.encode(content.toString(),"UTF-8");
			String webServiceURL = AppWindow.props.getProperty("POWebService.TermSearch.URL");
			webServiceURL = webServiceURL.replace("<search_term>", encodedContent);
			URL url = new URL(webServiceURL);
			HttpURLConnection connection = (HttpURLConnection) url.openConnection();
			BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()));
			// if the response from Web service is 'OK'
			if (connection.getResponseCode() == 200)
	        {
		        String inputLine;
		        JSONObject object = null;
		        while ((inputLine = in.readLine()) != null) 
		        {
		        	object = new JSONObject(inputLine);
		      	}
		        
		        JSONArray array = new JSONArray(object.getString("PO_term_search_response"));
		        for(int i=0; i<array.length();i++)
		        {
		        	OntologyTerm term = new OntologyTerm();
		        	term.setAccessionId(array.getJSONObject(i).getString("accession_id"));
		        	term.setName(formatizeToUnescapeHTML(array.getJSONObject(i).getString("match")));
		        	terms.add(term);
		        }
		        in.close();
	        }
	        else
	        {
	        	System.out.println("Response error");
	        }
	    }
	    catch(Exception ex)
	    {
	    }
	    return terms;
	}
	
	public static String formatizeToUnescapeHTML(String term)
	{
		Pattern pattern = Pattern.compile("&#[0-9]+");
	    Matcher matcher = pattern.matcher(term);
	    StringBuffer formattedTerm = new StringBuffer();
	    while (matcher.find()) {
	    	String matchedText = matcher.group();
	    	matcher.appendReplacement(formattedTerm, matchedText + ";");
	    }
	    matcher.appendTail(formattedTerm);
	    return formattedTerm.toString();
	}
	
	
	
	
	public  ArrayList<SpeciesTerm> getSpeciesTerms(String content) {
		ArrayList<SpeciesTerm> speciesTerms = new ArrayList<SpeciesTerm>();
		
        String namBankId,nameBankString;
		try
	    {
			String xmlContent = "";
			String encodedContent = URLEncoder.encode(content.toString(),"UTF-8");
			String webServiceURL = AppWindow.props.getProperty("UbioWebService.SpeciesTermSearch.URL");
			webServiceURL = webServiceURL.replace("<search_term>", encodedContent);
			URL url = new URL(webServiceURL);
			HttpURLConnection connection = (HttpURLConnection) url.openConnection();
			BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()));
			
			// if the response from Web service is 'OK'
			if (connection.getResponseCode() == 200)
	        {
				String inputLine;
				while ((inputLine = in.readLine()) != null) 
		        {
					xmlContent += inputLine;
				}
		        Document doc = loadXMLFromString(xmlContent);
		        Element docEle = doc.getDocumentElement();
		        NodeList nlist = docEle.getElementsByTagName("value");
				if(nlist != null && nlist.getLength() > 0) {
					for(int i = 0 ; i < nlist.getLength();i++) {
						//get the employee element
						Element el = (Element)nlist.item(i);
						namBankId = getTagValue("namebankID", el);
						nameBankString = new String(DatatypeConverter.parseBase64Binary(getTagValue("nameString", el)));
						SpeciesTerm species = new SpeciesTerm(nameBankString,namBankId);
						speciesTerms.add(species);
					}
				}
		        in.close();
	        }
	        else
	        {
	        	System.out.println("Response error");
	        }
	    }
	    catch(Exception ex)
	    {
	    }
	    return speciesTerms;
	}
	
    public static Document loadXMLFromString(String xml) throws Exception
    {
        DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
        DocumentBuilder builder = factory.newDocumentBuilder();
        InputSource is = new InputSource(new StringReader(xml));
        return builder.parse(is);
    }

    private static String getTagValue(String sTag, Element eElement) {
    	NodeList nlList = eElement.getElementsByTagName(sTag).item(0).getChildNodes();
     
            Node nValue = (Node) nlList.item(0);
     
    	return nValue.getNodeValue();
      }
	
	
}